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Improving the performance of Bayesian phylogenetic inference under relaxed clock models
BACKGROUND: Bayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms. RESULTS: This paper develops a new algorithm to i...
Autores principales: | , |
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Formato: | Online Artículo Texto |
Lenguaje: | English |
Publicado: |
BioMed Central
2020
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Materias: | |
Acceso en línea: | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222466/ https://www.ncbi.nlm.nih.gov/pubmed/32410614 http://dx.doi.org/10.1186/s12862-020-01609-4 |
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author | Zhang, Rong Drummond, Alexei |
author_facet | Zhang, Rong Drummond, Alexei |
author_sort | Zhang, Rong |
collection | PubMed |
description | BACKGROUND: Bayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms. RESULTS: This paper develops a new algorithm to improve the efficiency of Bayesian phylogenetic inference for models that include a per-branch rate parameter. In a Markov chain Monte Carlo algorithm, the presented proposal kernel changes evolutionary rates and divergence times at the same time, under the constraint that the implied genetic distances remain constant. Specifically, the proposal operates on the divergence time of an internal node and the three adjacent branch rates. For the root of a phylogenetic tree, there are three strategies discussed, named Simple Distance, Small Pulley and Big Pulley. Note that Big Pulley is able to change the tree topology, which enables the operator to sample all the possible rooted trees consistent with the implied unrooted tree. To validate its effectiveness, a series of experiments have been performed by implementing the proposed operator in the BEAST2 software. CONCLUSIONS: The results demonstrate that the proposed operator is able to improve the performance by giving better estimates for a given chain length and by using less running time for a given level of accuracy. Measured by effective samples per hour, use of the proposed operator results in overall mixing more efficient than the current operators in BEAST2. Especially for large data sets, the improvement is up to half an order of magnitude. |
format | Online Article Text |
id | pubmed-7222466 |
institution | National Center for Biotechnology Information |
language | English |
publishDate | 2020 |
publisher | BioMed Central |
record_format | MEDLINE/PubMed |
spelling | pubmed-72224662020-05-20 Improving the performance of Bayesian phylogenetic inference under relaxed clock models Zhang, Rong Drummond, Alexei BMC Evol Biol Methodology Article BACKGROUND: Bayesian MCMC has become a common approach for phylogenetic inference. But the growing size of molecular sequence data sets has created a pressing need to improve the computational efficiency of Bayesian phylogenetic inference algorithms. RESULTS: This paper develops a new algorithm to improve the efficiency of Bayesian phylogenetic inference for models that include a per-branch rate parameter. In a Markov chain Monte Carlo algorithm, the presented proposal kernel changes evolutionary rates and divergence times at the same time, under the constraint that the implied genetic distances remain constant. Specifically, the proposal operates on the divergence time of an internal node and the three adjacent branch rates. For the root of a phylogenetic tree, there are three strategies discussed, named Simple Distance, Small Pulley and Big Pulley. Note that Big Pulley is able to change the tree topology, which enables the operator to sample all the possible rooted trees consistent with the implied unrooted tree. To validate its effectiveness, a series of experiments have been performed by implementing the proposed operator in the BEAST2 software. CONCLUSIONS: The results demonstrate that the proposed operator is able to improve the performance by giving better estimates for a given chain length and by using less running time for a given level of accuracy. Measured by effective samples per hour, use of the proposed operator results in overall mixing more efficient than the current operators in BEAST2. Especially for large data sets, the improvement is up to half an order of magnitude. BioMed Central 2020-05-14 /pmc/articles/PMC7222466/ /pubmed/32410614 http://dx.doi.org/10.1186/s12862-020-01609-4 Text en © The Author(s) 2020 Open Access This article is licensed under a Creative Commons Attribution 4.0 International License, which permits use, sharing, adaptation, distribution and reproduction in any medium or format, as long as you give appropriate credit to the original author(s) and the source, provide a link to the Creative Commons licence, and indicate if changes were made. The images or other third party material in this article are included in the article’s Creative Commons licence, unless indicated otherwise in a credit line to the material. If material is not included in the article’s Creative Commons licence and your intended use is not permitted by statutory regulation or exceeds the permitted use, you will need to obtain permission directly from the copyright holder. To view a copy of this licence, visit http://creativecommons.org/licenses/by/4.0/. The Creative Commons Public Domain Dedication waiver (http://creativecommons.org/publicdomain/zero/1.0/) applies to the data made available in this article, unless otherwise stated in a credit line to the data. |
spellingShingle | Methodology Article Zhang, Rong Drummond, Alexei Improving the performance of Bayesian phylogenetic inference under relaxed clock models |
title | Improving the performance of Bayesian phylogenetic inference under relaxed clock models |
title_full | Improving the performance of Bayesian phylogenetic inference under relaxed clock models |
title_fullStr | Improving the performance of Bayesian phylogenetic inference under relaxed clock models |
title_full_unstemmed | Improving the performance of Bayesian phylogenetic inference under relaxed clock models |
title_short | Improving the performance of Bayesian phylogenetic inference under relaxed clock models |
title_sort | improving the performance of bayesian phylogenetic inference under relaxed clock models |
topic | Methodology Article |
url | https://www.ncbi.nlm.nih.gov/pmc/articles/PMC7222466/ https://www.ncbi.nlm.nih.gov/pubmed/32410614 http://dx.doi.org/10.1186/s12862-020-01609-4 |
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